The diamer in Gramicidin is seen showing the antiparallel hydrogen bonding between the amid hydrogens and carbonyl oxygens.
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Gramicidin

Gramicidin is a heterogeneous mixture of six antibiotic compounds divided into three catagories: Gramicidin A, B and C, all of which are obtained from the soil bacterial species Bacillus brevis and called collectily Gramicidin D. Gramicidin D are linear pentadecapeptides, that is, they are long protein chains made up of 15 amino acids. This is in contrast to Gramicidin S which is a cyclic peptide chain. more...

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Gramicidin is especially effective against gram-positive bacteria but induces hemolysis in lower concentrations than bacteria cell death thus cannot be administered internally. It is used primarily as a topical antibiotic and is one of the three constituents of consumer antibiotic Neosporin Ophthalmic Solution. In 1939 the American microbiologist René Dubos isolated the substance tyrothricin and later showed that it was composed of two substances, gramicidin (20%) and tyrocidine (80%). These were the first antibiotics to be manufactured commercially.

Gramicidin is composed of the general foruma: formyl-L-X-Gly-L-Ala-D-Leu-L-Ala-D-Val-L-Val-DVal-L-Trp-D-Leu-L-Y-D-Leu-L-Trp-D-Leu-L-Trp-ethanolamine

X and Y depend upon the gramicidin molecule. There exists valine and isoleucine variants of all three gramicidin species and 'X' can be either. Y determines which is which; in the place of Y Gramicidin A contains Tryptophan, B contains Phenylalanine and C contains Tyrosine. Also note the alternating stereochemical configurations (in the form of D and L) of the amino acids: this is vital to the formation of the ß-helix.

Gramicidin's bactericidal activity is a result of increasing the permeability of the bacterial cell wall allowing inorganic cations to travel through unrestricted, thereby destroying the ion gradient between the cytoplasm and the extracellular environment.

In gramicidin D, two strands are held end to end by hydrogen bonding within the cell bilayer. The alternating stereochemistry allows the amino acid functionalities to point outward creating a central pore which freely allows cations to pass. Thus gramicidin A is basically functions as a channel. The bound helix can insert itself into the lipid bilayer of a cell and destroy the ion gradient thereby killing the cell.

That gramicidin D functions as a channel was demonstrated by Hladky and Haydon, who investigated the unit conductance channel. In general, gramicidin channels are ideally selective for monovalent cations and the single-channel conductances for the alkali cations are ranked in the same order as the aqueous mobilities of these ions. Divalent cations like Ca-2+ block the channel by binding near the mouth of the channel. So it is basically impermeable to divalent cations. It also excludes anions. Cl- in particular is excluded from the channel because its hydration shell is thermodynamically stronger than that of most monovalent cations. The channel is permeable to most monovalent cations, which move through the channel in single file. The channel is filled with about six water molecules, almost all of which must be displaced when an ion is transported. Thus, ions moving through the gramicidin pore carry along a single file of water molecules. Such a flux of ion and water molecules is known as flux coupling. In the presence of a second type of permeable ion, the two ions couple their flux as well. Like Valinomycin and Nonactin, the gramicidin channel is selective for potassium over sodium but only slightly so. It has a permeability ration of 2.9. It is impermeable to anions but there are conditions under which some anion permeation may be observed. Its ability to bind and transport cations is due to the presence of cation-binding sites in the channel. Specifically, there are two such binding sites, one strong and the other weak.

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Gramicidin and Related Ion Channel-Forming Peptides - No. 225 $51.00 The effects of single amino acid replacements on the structure and function of the gramicidin A ion channel determined using nuclear magnetic resonance ... conductance measurements : (Dissertation) $55.00
Synthesis and single channel conductances of cyclopentane-dicarboxamid e linked gramicidin A dimers : (Dissertation) $55.00

Molecular Dynamics Simulations of C^sub 2^F^sub 6^ Effects on Gramicidin A: Implications of the Mechanisms of General Anesthesia
ABSTRACT It was recently postulated that the effects of general anesthetics on protein global dynamics might underlie a unitary molecular mechanism of ...
Effects of Phenylalanine Substitutions in Gramicidin A on the Kinetics of Channel Formation in Vesicles and Channel Structure in SDS Micelles
ABSTRACT The common occurrence of Trp residues at the aqueous-lipid interface region of transmembrane channels is thought to be indicative of its importance ...
Spin-Labeled Gramicidin A: Channel Formation and Dissociation
ABSTRACT Gramicidin A was studied by continuous wave electron spin resonance (CW-ESR) and by double-quantum coherence electron spin resonance (DQC-ESR) ...
Monitoring Gramicidin Conformations in Membranes: A Fluorescence Approach
ABSTRACT We have monitored the membrane-bound channel and nonchannel conformations of gramicidin utilizing red-edge excitation shift (REES), and related ...
NMR Studies of Lipid Lateral Diffusion in the DMPC/Gramicidin D/Water System: Peptide Aggregation and Obstruction Effects
ABSTRACT The PFG-NMR method has been used in macroscopically oriented bilayers to investigate the effect of the peptide gramicidin D on the lateral diffusion ...
Ionic Permeation Free Energy in Gramicidin: A Semimicroscopic Perspective
ABSTRACT Ion permeation through the gramicidin channel is studied using a model that circumvents two major difficulties inherent to standard simulational ...
Structural Restraints and Heterogeneous Orientation of the Gramicidin A Channel Closed State in Lipid Bilayers
ABSTRACT Although there have been several decades of literature illustrating the opening and closing of the monovalent cation selective gramicidin A channel ...
Orientation and Lipid-Peptide Interactions of Gramicidin A in Lipid Membranes: Polarized Attenuated Total Reflection Infrared Spectroscopy and Spin-Label
ABSTRACT Gramicidin A was incorporated at a peptide/lipid ratio of 1:10 mol/mol in aligned bilayers of dimyristoyl phosphatidylcholine (DMPC), phosphatidylserine ...

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